Abstract
Human papillomavirus (HPV) is a widespread and diverse group of viruses that are responsible for various clinical conditions, including cervical cancer, one of the most common cancers among women worldwide. In Africa, the prevalence and distribution of HPV genotypes vary significantly across different regions.
This study utilized a cohort comprising 9203 HPV sequences isolated from cervical samples across twenty-one African countries sourced from the National GenBank. Among these sequences were 1,347 HPV31 sequences from Rwanda; 879 HPV66, 782 HPV18 from Mauritius, 500 HPV31 from Guinea, 459 HPV45 from Senegal, 446 HPV18 from Tunisia, 445 HPV45 sequences from Cameroon, 445 HPV18 from Ghana, 445 HPV66 from Kenya, 442 from Algeria; 438 HPV35 from Zimbabwe, 364 HPV31, HPV16, HPV53, HPV83, HPV66, HPV62, and HPV89 sequences from Morocco, 351 from Chad, 340 HPV53/HPV6 sequences from Nigeria, 299 HPV16 from Gabon, 290 HPV45 sequences from Tanzania, 260 HPV18/HPV16 from Mali, 200 HPV58 sequences from Ethiopia, 35 from Congo, 20 HPV5 sequences from Egypt, and 10 HPV36 from Uganda. To refine the dataset and minimize redundancy, a stringent 99% sequence identity threshold was applied using CD-HIT, which identified184 unique sequences.
Employing the RAxML tool, a phylogenetic tree was meticulously crafted to scrutinize the evolutionary relationships inherent within the HPV sequences. Furthermore, a Python 3-generated heatmap rooted in multiple sequence alignment (MSA) was generated to elucidate discernible patterns and relationships among the HPV sequences.
The phylogenetic analysis demonstrated that African HPV sequences share genetic ancestry with European sequences, whereas American isolates serve as distinct outgroups. This interconnectedness underscores the intricate interplay of historical, regional, and cultural determinants that have collectively contributed to shaping the genomic landscape of African samples. The geographically variable HPV genotypes 35, 31, 16, 18, 58, 45, 7, and 66 are the most common in Africa. Algeria, Morocco, Rwanda, and Guinea are dispersed, but the rates of infection are highest in the Republic of Congo and Chad.